MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Rank	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 2458 to 2507 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
154	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Measured	Subtracted	1	9035	7279.6	1755.4
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Ranked	Divided	0	10883	12622.8	1.15986
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]		Subtracted		15395.7	16992.9	1597.2
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]		Divided	1	249.663	298.263	1.19466
	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158]	Squared	Subtracted		70525.9	52678.7	17847.2
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]		Divided		42788.3	60162.6	1.40605
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]			0	1110.11	669.13	1.65903
155	60s ribosomal protein l23a. [swissprot;acc:p29316]		Subtracted		2784.77	3420.27	635.5
	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	Measured			1162.21	1376.88	214.67
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Squared	Divided	1	126408	89940.5	1.40546
	cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]		Subtracted		70525.9	52678.7	17847.2
	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]	Rooted	Divided	0	14.232	16.6448	1.16953
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		Subtracted	1	54.2343	66.7323	12.498
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Measured	Divided		23693.7	18263	1.29736
	metaxin 1. [swissprot;acc:q13505]	Rooted	Subtracted	0	14.7289	11.2174	3.5115
	musashi 1. [refseq;acc:nm_002442]	Ranked		1	227.491	199.458	28.033
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Measured			9035	7279.6	1755.4
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	Ranked	Divided	0	12759.4	11028.8	1.15692
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]			1	249.663	298.263	1.19466
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Squared		0	21273.2	12858.5	1.65441
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Ranked	Subtracted		13248.5	11666.4	1582.1
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Rooted	Divided	1	55.7423	65.6839	1.17835
	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]	Measured		0	2230.13	1729.7	1.28932
156	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Squared	Subtracted		2785.55	3421.01	635.46
	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]			1	70525.9	52678.7	17847.2
	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]	Rooted	Divided	0	14.2464	16.6605	1.16945
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]		Subtracted	1	55.1026	67.5701	12.4675
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Measured	Divided		23693.7	18263	1.29736
	metaxin 1. [swissprot;acc:q13505]		Subtracted	0	933.395	723.368	210.027
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]			1	9035	7279.6	1755.4
	nuclear protein ukp68. [refseq;acc:nm_024824]	Ranked			227.491	199.458	28.033
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Squared	Divided	0	366.272	222.124	1.64895
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	Ranked		1	249.663	298.263	1.19466
	septin 10 isoform 1. [refseq;acc:nm_144710]	Squared			89578.7	125883	1.40528
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Rooted			56.3447	66.124	1.17356
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Ranked	Subtracted	0	13248.5	11666.4	1582.1
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Rooted			39.5626	36.099	3.4636
	tubby protein homolog. [swissprot;acc:p50607]	Ranked	Divided		12303.7	10641.7	1.15618
	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]	Measured			2230.13	1729.7	1.28932
157	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Squared	Subtracted		2569.37	3201.81	632.44
	brain protein 44. [swissprot;acc:o95563]		Divided	1	89182.8	125229	1.40418
	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	Rooted		0	14.2752	16.6919	1.16929
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]			1	52.7582	61.9123	1.17351
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Measured			23693.7	18263	1.29736
	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	Squared	Subtracted		76438	58889.7	17548.3
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Rooted			55.1113	67.5537	12.4424
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Ranked		0	11364	12941	1577
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Measured	Divided		261.105	336.584	1.28908
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]		Subtracted	1	9035	7279.6	1755.4
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Ranked			312	284	28

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.